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Epidemiological data of genital chlamydia and gonorrhea, required to inform design and implementation of control programs, are limited for rural Africa. There are no data on the prevalence of rectal or pharyngeal infections among African women.A cross-sectional study of 604 adult women visiting 25 primary health care facilities in rural South Africa was conducted. Vaginal, anorectal, and oropharyngeal swabs were tested for Chlamydia trachomatis and Neisseria gonorrhoeae.Prevalence of genital chlamydia was 16% and that of gonorrhea was 10%; rectal chlamydial infection was diagnosed in 7.1% and gonococcal in 2.5% of women. One woman had pharyngeal chlamydia. Most women with genital chlamydia (61%) and gonorrhea (57%) were asymptomatic. Independent risk factors for genital chlamydia were younger age (adjusted odds ratio [aOR], 0.96 per year; 95% confidence interval [CI], 0.93–0.98), hormonal contraceptive use (aOR, 2.2; 95% CI, 1.3–3.7), pregnancy (aOR, 2.4; 95% CI, 1.3–4.4), and intravaginal cleansing (aOR, 1.7; 95% CI, 1.04–2.8). Intravaginal cleansing was associated with genital gonorrhea (aOR, 1.9; 95% CI, 1.1–3.3).Genital and rectal, but not pharyngeal, chlamydia and gonorrhea are highly prevalent and frequently asymptomatic in women in rural South Africa. Young women attending health care facilities for antenatal care or family planning should be prioritized in control efforts.